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#!/bin/bash | ||
mv DESCRIPTION DESCRIPTION.old | ||
grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION | ||
mkdir -p ~/.R | ||
echo -e "CC=$CC | ||
FC=$FC | ||
CXX=$CXX | ||
CXX98=$CXX | ||
CXX11=$CXX | ||
CXX14=$CXX" > ~/.R/Makevars | ||
$R CMD INSTALL --build . |
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{% set version = "1.38.0" %} | ||
{% set name = "EBSeq" %} | ||
{% set bioc = "3.16" %} | ||
|
||
package: | ||
name: 'bioconductor-{{ name|lower }}' | ||
version: '{{ version }}' | ||
source: | ||
url: | ||
- 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' | ||
- 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' | ||
- 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' | ||
- 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' | ||
md5: 3dcbccf3dab22b82b2535991266b3f02 | ||
build: | ||
number: 0 | ||
rpaths: | ||
- lib/R/lib/ | ||
- lib/ | ||
noarch: generic | ||
requirements: | ||
host: | ||
- 'r-base >=4.1,<4.2' | ||
- r-blockmodeling | ||
- r-gplots | ||
- r-testthat | ||
run: | ||
- 'r-base >=4.1,<4.2' | ||
- r-blockmodeling | ||
- r-gplots | ||
- r-testthat | ||
test: | ||
commands: | ||
- '$R -e "library(''{{ name }}'')"' | ||
about: | ||
home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' | ||
license: Artistic-2.0 | ||
summary: 'An R package for gene and isoform differential expression analysis of RNA-seq data' | ||
description: 'Differential Expression analysis at both gene and isoform level using RNA-seq data' | ||
extra: | ||
identifiers: | ||
- biotools:ebseq | ||
- doi:10.1093/bioinformatics/btt087 | ||
parent_recipe: | ||
name: bioconductor-ebseq | ||
path: recipes/bioconductor-ebseq | ||
version: 1.20.0 | ||
|
29 changes: 29 additions & 0 deletions
29
recipes/libpng/0001-Include-pkg-config-files-in-the-Windows-packages-too.patch
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--- libpng-1.6.38.orig/CMakeLists.txt 2022-09-14 16:42:00.000000000 -0300 | ||
+++ libpng-1.6.38/CMakeLists.txt 2022-09-15 10:09:48.728794541 -0300 | ||
@@ -932,7 +932,7 @@ | ||
# We use the same files like ./configure, so we have to set its vars. | ||
# Only do this on Windows for Cygwin - the files don't make much sense | ||
# outside of a UNIX look-alike. | ||
-if(NOT WIN32 OR CYGWIN OR MINGW) | ||
+if(1) | ||
set(prefix ${CMAKE_INSTALL_PREFIX}) | ||
set(exec_prefix ${CMAKE_INSTALL_PREFIX}) | ||
set(libdir ${CMAKE_INSTALL_FULL_LIBDIR}) | ||
@@ -1016,13 +1016,13 @@ | ||
install(FILES png.5 | ||
DESTINATION ${CMAKE_INSTALL_MANDIR}/man5) | ||
# Install the pkg-config files. | ||
+ install(FILES ${CMAKE_CURRENT_BINARY_DIR}/libpng.pc | ||
+ DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig) | ||
+ install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${PNGLIB_NAME}.pc | ||
+ DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig) | ||
if(NOT CMAKE_HOST_WIN32 OR CYGWIN OR MINGW) | ||
- install(FILES ${CMAKE_CURRENT_BINARY_DIR}/libpng.pc | ||
- DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig) | ||
install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/libpng-config | ||
DESTINATION ${CMAKE_INSTALL_BINDIR}) | ||
- install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${PNGLIB_NAME}.pc | ||
- DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig) | ||
install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/${PNGLIB_NAME}-config | ||
DESTINATION ${CMAKE_INSTALL_BINDIR}) | ||
endif() |
29 changes: 29 additions & 0 deletions
29
recipes/libpng/0002-Ensure-that-lm-is-not-included-in-Windows-pkg-config.patch
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From ed4def04ed595c83ed8082845f5b807413b9400f Mon Sep 17 00:00:00 2001 | ||
From: Mark Harfouche <[email protected]> | ||
Date: Wed, 6 Jul 2022 17:13:50 -0400 | ||
Subject: [PATCH 2/2] Ensure that -lm is not included in Windows pkg-config | ||
|
||
--- | ||
CMakeLists.txt | 6 +++++- | ||
1 file changed, 5 insertions(+), 1 deletion(-) | ||
|
||
diff --git a/CMakeLists.txt b/CMakeLists.txt | ||
index 25e9e4d4e..649698ff6 100644 | ||
--- a/CMakeLists.txt | ||
+++ b/CMakeLists.txt | ||
@@ -825,7 +825,11 @@ if(1) | ||
set(exec_prefix ${CMAKE_INSTALL_PREFIX}) | ||
set(libdir ${CMAKE_INSTALL_FULL_LIBDIR}) | ||
set(includedir ${CMAKE_INSTALL_FULL_INCLUDEDIR}) | ||
- set(LIBS "-lz -lm") | ||
+ if(NOT "${M_LIBRARY}" STREQUAL "") | ||
+ set(LIBS "-lz -lm") | ||
+ else() | ||
+ set(LIBS "-lz") | ||
+ endif() | ||
configure_file(${CMAKE_CURRENT_SOURCE_DIR}/libpng.pc.in | ||
${CMAKE_CURRENT_BINARY_DIR}/${PNGLIB_NAME}.pc @ONLY) | ||
create_symlink(libpng.pc FILE ${PNGLIB_NAME}.pc) | ||
-- | ||
2.34.1 | ||
|
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mkdir build-%SUBDIR%-%c_compiler% | ||
cd build-%SUBDIR%-%c_compiler% | ||
|
||
:: Configure. | ||
cmake -G Ninja ^ | ||
-D CMAKE_INSTALL_PREFIX=%LIBRARY_PREFIX% ^ | ||
-D ZLIB_LIBRARY=%LIBRARY_LIB%\zlib.lib ^ | ||
-D ZLIB_INCLUDE_DIR=%LIBRARY_INC% ^ | ||
-DCMAKE_C_FLAGS="%CFLAGS% -DWIN32" ^ | ||
-DCMAKE_BUILD_TYPE=Release ^ | ||
%SRC_DIR% | ||
if errorlevel 1 exit /b 1 | ||
|
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cmake --build . --target install | ||
if errorlevel 1 exit /b 1 | ||
|
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:: Test. | ||
ctest -C Release | ||
if errorlevel 1 exit 1 | ||
|
||
:: Make copies of the .lib files without the embedded version number. | ||
copy %LIBRARY_LIB%\libpng16.lib %LIBRARY_LIB%\libpng.lib | ||
if errorlevel 1 exit 1 | ||
|
||
copy %LIBRARY_LIB%\libpng16_static.lib %LIBRARY_LIB%\libpng_static.lib | ||
if errorlevel 1 exit 1 | ||
|
||
:: Make copies of the .lib files without the 'lib' prefix. | ||
copy %LIBRARY_LIB%\libpng16.lib %LIBRARY_LIB%\png16.lib | ||
if errorlevel 1 exit 1 | ||
|
||
copy %LIBRARY_LIB%\libpng16_static.lib %LIBRARY_LIB%\png16_static.lib | ||
if errorlevel 1 exit 1 | ||
|
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#!/bin/bash | ||
# Get an updated config.sub and config.guess | ||
cp $BUILD_PREFIX/share/libtool/build-aux/config.* . | ||
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||
export CFLAGS="$CFLAGS -I$PREFIX/include -L$PREFIX/lib" | ||
export CPPFLAGS="$CPPFLAGS -I$PREFIX/include" | ||
|
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./configure --prefix=$PREFIX \ | ||
--with-zlib-prefix=$PREFIX | ||
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make -j${CPU_COUNT} ${VERBOSE_AT} | ||
if [[ "${CONDA_BUILD_CROSS_COMPILATION}" != "1" ]]; then | ||
make check | ||
fi | ||
make install | ||
|
||
# We can remove this when we start using the new conda-build. | ||
find $PREFIX -name '*.la' -delete |
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BUILD: aarch64-conda_cos7-linux-gnu | ||
CI: azure | ||
c_compiler: gcc | ||
c_compiler_version: '10' | ||
cdt_arch: aarch64 | ||
cdt_name: cos7 | ||
channel_sources: conda-forge | ||
channel_targets: conda-forge main | ||
cpu_optimization_target: nocona | ||
cran_mirror: https://cran.r-project.org | ||
cxx_compiler: gxx | ||
docker_image: quay.io/condaforge/linux-anvil-aarch64 | ||
extend_keys: | ||
- pin_run_as_build | ||
- ignore_version | ||
- ignore_build_only_deps | ||
- extend_keys | ||
fortran_compiler: gfortran | ||
ignore_build_only_deps: | ||
- numpy | ||
- python | ||
lua: '5' | ||
numpy: '1.16' | ||
perl: 5.26.2 | ||
pin_run_as_build: | ||
python: | ||
min_pin: x.x | ||
max_pin: x.x | ||
r-base: | ||
min_pin: x.x | ||
max_pin: x.x | ||
zlib: | ||
max_pin: x.x | ||
python: '3.9' | ||
r_base: '3.5' | ||
target_platform: linux-aarch64 | ||
zlib: '1.2' |
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index: libpng-1.6.36/pngread.c | ||
=================================================================== | ||
--- libpng-1.6.36.orig/pngread.c 2018-12-01 15:36:00.000000000 +0100 | ||
+++ libpng-1.6.36/pngread.c 2019-01-28 12:41:14.044709070 +0100 | ||
@@ -994,6 +994,11 @@ png_read_destroy(png_structrp png_ptr) | ||
png_ptr->chunk_list = NULL; | ||
#endif | ||
|
||
+#if PNG_ARM_NEON_IMPLEMENTATION == 1 | ||
+ png_free(png_ptr, png_ptr->riffled_palette); | ||
+ png_ptr->riffled_palette = NULL; | ||
+#endif | ||
+ | ||
/* NOTE: the 'setjmp' buffer may still be allocated and the memory and error | ||
* callbacks are still set at this point. They are required to complete the | ||
* destruction of the png_struct itself. |
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# This file created by conda-build 3.22.0 | ||
# meta.yaml template originally from: | ||
# /home/conda/recipe_root, last modified Fri Sep 16 16:57:13 2022 | ||
# ------------------------------------------------ | ||
|
||
package: | ||
name: libpng | ||
version: 1.6.38 | ||
source: | ||
patches: | ||
- 0001-Include-pkg-config-files-in-the-Windows-packages-too.patch | ||
- 0002-Ensure-that-lm-is-not-included-in-Windows-pkg-config.patch | ||
- libpng-arm-free.patch | ||
sha256: e2b5e1b4329650992c041996cf1269681b341191dc07ffed816c555769cceb77 | ||
url: http://download.sourceforge.net/libpng/libpng-1.6.38.tar.gz | ||
build: | ||
number: '0' | ||
run_exports: | ||
- libpng >=1.6.38,<1.7.0a0 | ||
string: hf9034f9_0 | ||
requirements: | ||
build: | ||
- _openmp_mutex 4.5 2_gnu | ||
- autoconf 2.69 pl5321h689fa9f_11 | ||
- automake 1.16.5 pl5321h8af1aa0_0 | ||
- binutils_impl_linux-aarch64 2.36.1 h026399b_2 | ||
- binutils_linux-aarch64 2.36 h7854541_10 | ||
- gcc_impl_linux-aarch64 10.4.0 hbc23e19_16 | ||
- gcc_linux-aarch64 10.4.0 h72ad2ee_10 | ||
- kernel-headers_linux-aarch64 4.18.0 h5b4a56d_13 | ||
- ld_impl_linux-aarch64 2.36.1 h02ad14f_2 | ||
- libgcc-devel_linux-aarch64 10.4.0 hf691355_16 | ||
- libgcc-ng 12.1.0 h3242a24_16 | ||
- libgomp 12.1.0 h3242a24_16 | ||
- libnsl 2.0.0 hf897c2e_0 | ||
- libsanitizer 10.4.0 h69a60c7_16 | ||
- libstdcxx-ng 12.1.0 hd01590b_16 | ||
- libtool 2.4.6 h01db608_1008 | ||
- m4 1.4.18 h516909a_1001 | ||
- make 4.3 h309ac5b_1 | ||
- perl 5.32.1 2_hf897c2e_perl5 | ||
- sysroot_linux-aarch64 2.17 h43d7e78_13 | ||
host: | ||
- _openmp_mutex 4.5 2_gnu | ||
- libgcc-ng 12.1.0 h3242a24_16 | ||
- libgomp 12.1.0 h3242a24_16 | ||
- libzlib 1.2.12 h4e544f5_3 | ||
- zlib 1.2.12 h4e544f5_3 | ||
run: | ||
- libgcc-ng >=12 | ||
- libzlib >=1.2.12,<1.3.0a0 | ||
test: | ||
commands: | ||
- test -f ${PREFIX}/lib/libpng.a | ||
- test -f ${PREFIX}/lib/libpng${SHLIB_EXT} | ||
- libpng-config --version | ||
about: | ||
description: 'libpng is the official PNG reference library. It supports almost all | ||
PNG | ||
features, is extensible, and has been extensively tested for over 20 years. | ||
' | ||
dev_url: https://sourceforge.net/p/libpng/code/ci/libpng16/tree/ | ||
doc_url: http://www.libpng.org/pub/png/libpng.html | ||
home: http://www.libpng.org/pub/png/libpng.html | ||
license: zlib-acknowledgement | ||
license_file: LICENSE | ||
license_url: http://www.libpng.org/pub/png/src/libpng-LICENSE.txt | ||
summary: PNG reference library | ||
extra: | ||
copy_test_source_files: true | ||
final: true | ||
recipe-maintainers: | ||
- msarahan | ||
- ocefpaf | ||
- pkgw |
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{% set version = "1.6.38" %} | ||
|
||
package: | ||
name: libpng | ||
version: {{ version }} | ||
|
||
source: | ||
url: http://download.sourceforge.net/libpng/libpng-{{ version }}.tar.gz | ||
sha256: e2b5e1b4329650992c041996cf1269681b341191dc07ffed816c555769cceb77 | ||
patches: | ||
- 0001-Include-pkg-config-files-in-the-Windows-packages-too.patch | ||
- 0002-Ensure-that-lm-is-not-included-in-Windows-pkg-config.patch | ||
- libpng-arm-free.patch # [aarch64] | ||
|
||
build: | ||
number: 0 | ||
skip: true # [win and vc<14] | ||
run_exports: | ||
# SO name changes at minor rev bumps. | ||
- {{ pin_subpackage('libpng', max_pin='x.x') }} | ||
|
||
requirements: | ||
build: | ||
- make # [unix] | ||
- cmake # [win] | ||
- m2-patch # [win] | ||
- ninja # [win] | ||
- libtool # [not win] | ||
- automake # [not win] | ||
- libtool # [unix] | ||
- {{ compiler('c') }} | ||
host: | ||
- zlib | ||
|
||
test: | ||
commands: | ||
- test -f ${PREFIX}/lib/libpng.a # [not win] | ||
- test -f ${PREFIX}/lib/libpng${SHLIB_EXT} # [not win] | ||
- libpng-config --version # [not win] | ||
|
||
about: | ||
home: http://www.libpng.org/pub/png/libpng.html | ||
license: zlib-acknowledgement | ||
license_file: LICENSE | ||
license_url: http://www.libpng.org/pub/png/src/libpng-LICENSE.txt | ||
summary: PNG reference library | ||
description: | | ||
libpng is the official PNG reference library. It supports almost all PNG | ||
features, is extensible, and has been extensively tested for over 20 years. | ||
doc_url: http://www.libpng.org/pub/png/libpng.html | ||
dev_url: https://sourceforge.net/p/libpng/code/ci/libpng16/tree/ | ||
|
||
extra: | ||
recipe-maintainers: | ||
- ocefpaf | ||
- msarahan | ||
- pkgw |
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BSD-3-Clause license | ||
Copyright (c) 2015-2022, conda-forge contributors | ||
All rights reserved. | ||
|
||
Redistribution and use in source and binary forms, with or without | ||
modification, are permitted provided that the following conditions are met: | ||
|
||
1. Redistributions of source code must retain the above copyright notice, | ||
this list of conditions and the following disclaimer. | ||
2. Redistributions in binary form must reproduce the above copyright | ||
notice, this list of conditions and the following disclaimer in the | ||
documentation and/or other materials provided with the distribution. | ||
3. Neither the name of the copyright holder nor the names of its | ||
contributors may be used to endorse or promote products derived from | ||
this software without specific prior written permission. | ||
|
||
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" | ||
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE | ||
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE | ||
ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS BE LIABLE FOR | ||
ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL | ||
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR | ||
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER | ||
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT | ||
LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY | ||
OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH | ||
DAMAGE. |
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